The Swedish cyberpunk comic Det osynliga kriget ("The Invisible War") turns out to be about a war fought with nanotech robots - destroying factories and infrastructure by making buildings fall down. To the public, that's just sloppy building practices that are part of their already Crapsack World.

Fan Fiction

Fittingly enough, a Secret War is what a 40k fanfiction called Secret War is all about.

Film

The war between vampires and lycans in the Underworld series is kept out of public knowledge, partly thanks to the Cleaners, a group made up of elite human soldiers and headed by the first immortal Alexander Corvinus. Their job is to work behind the scenes to clean up the mess the immortals leave behind. Following the third movie, where Corvinus dies and the Cleaners are all killed, humanity discovers vampires and werewolves and embarks on a full-scale genocide after there's no one left to clean up the two sides' messes.

Also, the war between vampires and one very angry half-vampire in Blade

Blade: You better wake up. The world you live in is just a sugar-coated topping! There is another world beneath it - the real world. And if you wanna survive it, you better learn to pull the trigger!

It is somewhat helped by the fact that the actual war is long over — it's just that the cats (and, it is implied in the sequel, the dogs as well) have their rogues who try to restart the war and win it in one go.

In Hellboy, it's mentioned in passing that World War II was simply the public front of the Occult War, which only came to an end with Adolf Hitler's real death in 1958.

The war between the Legions of Hell and the Gargoyle Order (created by Archangel Michael to fight the demons) in I, Frankenstein has been going on for centuries, if not millennia (it's stated by the gargoyles' leader that the demons were released on earth during Lucifer's rebellion). Both sides are vulnerable to one another (demons can only be "descended" by weapons marked with the gargoyle sigil, while gargoyles can only be "ascended" by beings without a soul, like demons and Adam). There are finite numbers on both sides, and no reinforcements are coming (although the demons are working to correct that oversight), and attrition has been slowly eating away at both sides, although there are still more demons than gargoyles. While the demons do employ unwitting humans for some tasks, they cannot use them as foot soldiers, since humans are unable to "ascend" gargoyles; the gargoyles won't use humans because they believe that human life is sacred (in fact, they give Adam a What the Hell, Hero? speech after his fight with demons in an alley results in the death of a human).

Harry Potter: The war between the wizards. Half-Blood Prince shows that the Prime Minister (and likely the Queen as well) are made aware of it after a number of incidents and disasters happen due to Voldemort (such as huge amounts of fog meaning breeding Dementors and a highly destructive "tornado" is actually the work of rampaging giants).

The war between the Muineers and the mutineer-Mutineers in the first Empire from the Ashes book, which has been going on since the dawn of human civilization. By the end of the book, it has become very, very not secret—people don't know what the hell is going on, but they sure can see the mayhem.

Fyodor Berezin's The Lunar Option describes battles on the Moon between the American astronauts and the Soviet cosmonauts during the 60s, after the discovery of an alien artifact. Obviously, no one in the general public is aware of this.

Several of these in The Dresden Files, primarily among them the war between the White Council of Wizards and the Vampire Courts. There's also an even more secret war known as the Oblivion War, whereby a secret brotherhood known as the Venatori wage a conflict in order to eliminate all knowledge of certain monstrous entities, as knowledge of them possessed by mortals connects the entities to the real world.

The various Weird Wars in the Diogenes Club stories by Kim Newman. Every so often an evil Great Enchanter arises, and it's the Club's job to put him down again.

If won, it would only be written of in the secret histories. If lost, there would be no more histories, secret or otherwise.

The war against the Yeerks in Animorphs. Until everything gets blown wide open in the end of the series.

The war between the Prophus and the Genjix in The Lives Of Tao, raging from the Spanish Inquisition to the modern day. Secrecy goes out the window when the Genjix openly attack Washington D.C. at the end of the second book. and the Prophus agents who survive tear down the Masquerade in retaliation.

The conflict between Light and Dark Others in Lukyanenko's Night Watch. Although it has become more of a cold war with the occasional black operation or two after the treaty that established both Watches and the Inquisition.

Several Cthulhu Mythos stories take this approach, drawing inspiration from The Shadow Over Innsmouth where the Marines were called in to clear out the Deep Ones after the events portrayed in the story. Subverted in Once More from the Top by A. Scott Glancy about some Men in Black interviewing one of the surviving members of that operation. He asks if they're winning the secret war that's obviously being fought — the MIB's tell him yes, not revealing that the politicians decided to bury the truth about Innsmouth rather than confront it, and the reason he's being interviewed is that all the files were destroyed and the war is hidden not only from the public, but the politicians as well, conducted with whatever resources they can beg, borrow or steal.

In The Laundry Files, The Laundry fights such a war on behalf of Britain. Other governments have their own secret magical agencies.

Fyodor Berezin's The Lunar Option details the discovery of an alien artifact on the Moon in The '70s, starting a secret space race between the two superpowers for its possession. The battles taking place in space and on the Moon involve many of the well-known astronauts and cosmonauts, including those who are officially listed as deceased.

The Eugenics Wars went unnoticed by the population at large. When they saw the brushfire wars of the 1990s, they were really seeing the children of Chrysalis trying to take over the world.

In Armada, the governments of Earth, under the umbrella of the Earth Defense Alliance, have been at war with mysterious aliens from Europa for decades. While most of it has been preparations for the actual all-out war, there have been a number of alien attacks on both Earth and the Moon.

Live Action TV

In the Stargate-verse the US is involved in interstellar conflicts, and doesn't even tell the heads of other nations at first, never mind the world at large. In various alternate timelines where the Secret War becomes a Non-Secret War, things often start to go very badly (such as in the Continuum movie, where Earth is full-on invaded by the Goa'uld).

A number of the UNIT stories in Doctor Who work this way, particularly in the classic series.

In the War of the Worlds series, only a handful of military, intelligence and science personnel know about the alien invasion coming out of dormancy. In the second series, the new aliens appear more human and are able to operate openly, since it's become such a Crapsack World that to most people they're indistinguishable from the corrupt corporations and organized crime.

Alphas has the fight between the alpha terrorist organization Red Flag and the Department of Defense and their own alpha team. In the first season finale Rosen breaks the masquerade, realizing that this secrecy ensures conflict where it might be avoided, facilitates atrocities on both sides, and is exactly what the Big Bad alpha Stanton Parish wants.

In UFO, humanity is in a low-key state of war with the aliens operating the UFOs, who are constantly trying to infiltrate the earth and kidnap humans. Since revealing this to the public would case wide-spread panic, a top-secret organisation, SHADO, is responsible both for the actual fighting and for covering up all evidence of alien activity.

Old World of Darkness is rife with secret war, going down between virtually every species of supernatural being, between different factions within the same species, and between supernaturals in general and those few groups of mortals who have been clued in to their existence.

Nephilim. The eons old combat between the title characters and the secret societies hunting them.

Call of Cthulhu supplement Glozel Est Authentique, adventure "Secrets of the Kremlin''. The Nodens Brotherhood has long opposed a cult that worships Shub-Niggurath.

On the subject of Call of Cthulhu, the entire Delta Green third-party supplement. Delta Green versus MJ-12, with a second front against the Karotechia (who occasionally also conflicts with MJ-12) and the odd fight or two against a random Mythos cult.

Chill. S.A.V.E. (Societas Albae Viae Eterniata AKA The Eternal Society of the White Way) does battle with supernatural creatures from The Unknown.

Feng Shui has a secret war that spans at least four different junctures in time, along with the Netherworld that connects these junctures, each with their own different factions vying for the power to remake human history in their image.

The game Conspiracy X also has a secret war involving reptilian aliens and other weirdness.

The Shadowrun universe has rival Mega Corps waging a covert war against each other, with the titular Shadowrunners being the deniable assets that the corps call upon to do their dirty work.

GURPS Black Ops. The PCs all work for "The Company", a secret organization with the twin objectives of 1) Kill all the aliens/psis/monsters trying to take over and 2) Don't let anyone outside The Company find out about the aliens/psis/monsters trying to take over.

The Infinite Worlds default setting has the two factions of Centrum and the Infinity Patrol who oppose each other at every turn and vie for control and influence on low-tech worlds, all while trying not to be detected by the natives of that timeline and expose their own existence.

Cthulhutech gets crazy with the strength of their Extra-Strength Masquerade. The shadow war between the Eldritch Society and the Chrysalis Corporation taking place within the arcologies and suburbs of the NEG-controlled areas is one thing, and the Chrysalis Corporation are very good at keeping things under wraps and discrediting or eating anyone who knows too much and might actually expose anything (plus, they have the leverage to have the government censor Dhohanoid-related reporting to prevent public panic). However, not only are Eldritch Abomination cults are alive and well, but one has formed a military force that has conquered China, under wraps, and the fact that the last Aeon War is still going on and the Migou are attacking again with a force equal to the one that nearly took Earth apart the last time. And the NEG can recruit people to fight on the China front without them knowing a thing about the war until they're already in too deep to back out.

In Unknown Armies this is the default state of the Occult Underground. Being composed of very driven, obsessed and, a lot of times, outright insane people, the Underground in most cities is either in constant conflict between the different cabals, or is just at the tipping point of an all out war.

In Rocket Age the Great Powers of Earth are currently fighting secret battles in the skies of Jupiter for the approval of the Europans.

Video Games

In the Assassin's Creed series, there is an ongoing, secret war between the Assassins and the Templars, which has been waged since the beginning of the human species, ever since humanity first rebelled against Those Who Came Before.

The war between the Forgotten and Abaddon's forces in Guild Wars: Nightfall qualifies. The Forgotten have spent the last thousand years fighting a slowly-losing war to keep Abaddon and his followers bound in the Realm of Torment. As of present, they maintain only scattered outposts in either dimension.

The Order of Whispers was founded to pursue such conflicts. They have watched over Palawa Joko's tomb, kept the existence of Abaddon and his demons from public knowledge, and a century before the game even interrogated and imprisoned a Titan.

Callof Duty Black Ops takes place entirely from the perspective of SOG operatives during the Cold War, predominantly in Vietnam. In addition to taking part in openly historic events like the Tet Offensive, the player attempts to assassinate Fidel Castro (which fails), sabotage a Soviet space program (which succeeds), and uncover the truth behind a brainwashing scheme that he himself is victim to. The game even emphasizes its covert overtones by redacting the character, location, and date information displayed at the beginning of every mission.

Dragon Age: Inquisitionreveals that the ancient elves fought among themselves long before the Tevinter Imperium invaded, and kept it a secret from the outside world. After losing knowledge of it and virtually everything else after the fall of their civilization the only people who know of it are the ancient elves guarding the temple of Mythal.

As the name implies Deus Ex: Invisible War focuses on a shadowy conflict between several clandestine groups over the future of humanity. The player can end up siding with any faction or even Kill 'em All.

The events of Deus Ex: Human Revolution fit the bill as well, perhaps more so. A character even comments that the term Invisible War is the best way to describe the events of Human Revolution.

Star Wars: The Old Republic: On Makeb, the Empire wages one against the Archon, the secret advisor to the Hutt Cartel all the while trying to keep their activities hidden from the Republic.

The XCOM games revolve around an alien invasion of the Earth, which XCOM, as a top-secret organization, is attempting to fight. While the first games are more in line with this, games like XCOM: Enemy Unknowngoes more public with it. After a certain point in the story the aliens start using Terror Attacks, which are open, outright brutal assaults on human cities. Enemy Unknown's Situation Room gives you a good indication of exactly how secret it is.

In Avatar: The Last Airbender, the war is secret to the Earth King only. The Dai Li took pains to make sure it stayed that way to keep the people of Ba Sing Se from going into a panic and to limit the capital's involvement with the war that would screw up their way of living.

Its hinted that while the Earth King is kept from knowing to make him a puppet, that many of the rest of the citizens don't know either. Brainwashing and control of information keep knowledge down, and constant fear makes those who do know too afraid to talk.

In Beast Wars, the Decepticon Megatron's message mentions the conflict between the Earthbound Transformers being a secret war. However, while it was the case in early issues of the comic, it was dropped in later issues, and in the cartoon, it's anything but covert in their interactions with humans (and Beast Wars is intentionally vague about which version is their past). While this could be an error, it's possible in this continuity, the conflict truly was a secret war, with only a few human allies (including the Witwickys) as Secret Keepers.

Visual Novels

The Holy Grail War in the Fate series of visual novels, games, light novels, etc. Interestingly enough, even to most of the Mage's Association itself, the war is mostly something of a rumour, and only higherups or people who do their research are fully aware of it.

Real Life

Real Life: CIA vs. KGB, CIA vs. Al-Qaeda, etc. The public only knows a very little about what really goes on behind the scenes.

It's at least a partial aversion, since it was public knowledge that the US intelligence community was working against enemies of the state. It's also subverted by the release of declassified documents that detail past black operations.

During the Vietnam War the CIA had a whole lot of things going on, including the Phoenix Program: a program of infiltration, capture, terrorism, and assassination.

The Laotian Civil War was termed the "Secret War", for much of the same reasons as the CIA's involvement in Vietnam.

During World War II, there was a secret war (With a book and documentary series with that title) where Allied scientists and engineers matched wits with their Axis counterparts to top and counter each other's inventions. Ultimately, the Allied side proved much better in this contest.

The Great Game between Imperial Russia and Victorian Britain in the 19th Century, which was more or less a precursor to the Cold War. It was mostly fought through proxies in Central Asia, occasionally spilling into regional conflicts like the Anglo-Afghan Wars, but never into direct confrontation between the two empires.

Many conspiracy theories suggest this. Especially those involving occultism, because any occultist system is seen as a kind of transformation/ conversion tool, which is able to produce results in both directions, good and bad. Because of this, conspiracy theorists tend to suggest that there is a war between those who want to save mankind and those who essentially want to destroy the human mind.

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